def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
self.checksum=md5sum(sys.argv[0])
self.checksum=self.checksum[-4:]
pyTecan=os.path.dirname(os.path.realpath(__file__))
self.gitlabel=strip(subprocess.check_output(["git", "describe","--always"],cwd=pyTecan))
worklist.comment("Generated %s (%s-%s pyTecan-%s)"%(datetime.now().ctime(),sys.argv[0],self.checksum,self.gitlabel))
worklist.userprompt("The following reagent tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt("The following eppendorf tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',subject='Run started (Generate: %s) expected runtime %.0f minutes'%(datetime.now().ctime(),clock.totalTime/60.0 if clock.totalTime is not None else 0.0 ) )
worklist.email(dest='*****@*****.**',subject='Tecan error',onerror=1)
self.cleanTips=0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis=False
self.ptcrunning=False
self.overrideSanitize=False
self.pgmStartTime=None
self.pgmEndTime=None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt("Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms=[]
self.timerStartTime=[None]*8
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
worklist.comment("Generated %s" % (datetime.now().ctime()))
worklist.userprompt(
"The following reagent tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt(
"The following eppendorf tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',
subject='Run started (Generate: %s)' %
(datetime.now().ctime()))
worklist.email(dest='*****@*****.**',
subject='Tecan error',
onerror=1)
self.cleanTips = 0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis = False
self.ptcrunning = False
self.overrideSanitize = False
self.pgmStartTime = None
self.pgmEndTime = None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt(
"Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms = []
self.timerStartTime = [None] * 8
def waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime-clock.pipetting > 120:
# Run any idle programs
oldElapsed=clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime-clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime-clock.pipetting-120)
if oldElapsed==clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime+=(clock.pipetting-self.pgmStartTime)
clock.thermotime+=(self.pgmEndTime-clock.pipetting)
clock.pipetting=self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
self.lihahome()
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
self.ptcrunning=False
self.moveplate(decklayout.SAMPLEPLATE,"Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.ENDTOSAFE,False,worklist.OPEN,worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15,1,5,True)
def setreagenttemp(self,temp=None):
if temp is None:
worklist.pyrun("RIC\\ricset.py IDLE")
decklayout.REAGENTPLATE.liquidTemp=22.7
else:
worklist.variable("dewpoint",temp,userprompt="Enter dewpoint",minval=0,maxval=20)
worklist.variable("rictemp","~dewpoint~+2")
worklist.pyrun("RIC\\ricset.py ~rictemp~")
decklayout.REAGENTPLATE.liquidTemp=temp+2 # Assumes that temp is the one used
def setreagenttemp(self, temp=None):
if temp is None:
worklist.pyrun("RIC\\ricset.py IDLE")
decklayout.REAGENTPLATE.liquidTemp = 22.7
else:
worklist.variable("dewpoint",
temp,
userprompt="Enter dewpoint",
minval=0,
maxval=20)
worklist.variable("rictemp", "~dewpoint~+2")
worklist.pyrun("RIC\\ricset.py ~rictemp~")
decklayout.REAGENTPLATE.liquidTemp = temp + 2 # Assumes that temp is the one used
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
worklist.comment("Generated %s"%(datetime.now().ctime()))
worklist.userprompt("The following reagent tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt("The following eppendorf tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',subject='Run started (Generate: %s)'%(datetime.now().ctime()))
worklist.email(dest='*****@*****.**',subject='Tecan error',onerror=1)
self.cleanTips=0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis=False
self.ptcrunning=False
self.overrideSanitize=False
self.pgmStartTime=None
self.pgmEndTime=None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt("Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms=[]
self.timerStartTime=[None]*8
def runpgm(self,pgm,duration,waitForCompletion=True,volume=10,hotlidmode="TRACKING",hotlidtemp=1):
if self.ptcrunning:
logging.error("Attempt to start a progam on PTC when it is already running")
if len(pgm)>8:
logging.error("PTC program name (%s) too long (max is 8 char)"%pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt="run %s"%pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE,"PTC")
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode=="TRACKING" or hotlidmode=="CONSTANT"
assert (hotlidmode=="TRACKING" and hotlidtemp>=0 and hotlidtemp<=45) or (hotlidmode=="CONSTANT" and hotlidtemp>30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d'%(pgm,hotlidmode,hotlidtemp,volume))
self.pgmStartTime=clock.pipetting
self.pgmEndTime=duration*60+clock.pipetting
self.ptcrunning=True
Sample.addallhistory("{%s}"%pgm,addToEmpty=False,onlyplate=decklayout.SAMPLEPLATE.name)
if waitForCompletion:
self.waitpgm()
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
self.checksum = md5sum(sys.argv[0])
self.checksum = self.checksum[-4:]
pyTecan = os.path.dirname(os.path.realpath(__file__))
self.gitlabel = strip(
subprocess.check_output(["git", "describe", "--always"],
cwd=pyTecan))
worklist.comment("Generated %s (%s-%s pyTecan-%s)" %
(datetime.now().ctime(), sys.argv[0], self.checksum,
self.gitlabel))
worklist.userprompt(
"The following reagent tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt(
"The following eppendorf tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(
dest='*****@*****.**',
subject='Run started (Generate: %s) expected runtime %.0f minutes'
% (datetime.now().ctime(),
clock.totalTime / 60.0 if clock.totalTime is not None else 0.0))
worklist.email(dest='*****@*****.**',
subject='Tecan error',
onerror=1)
self.cleanTips = 0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis = False
self.ptcrunning = False
self.overrideSanitize = False
self.pgmStartTime = None
self.pgmEndTime = None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt(
"Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms = []
self.timerStartTime = [None] * 8
def runpgm(self,
pgm,
duration,
waitForCompletion=True,
volume=10,
hotlidmode="TRACKING",
hotlidtemp=1):
if self.ptcrunning:
logging.error(
"Attempt to start a progam on PTC when it is already running")
if len(pgm) > 8:
logging.error("PTC program name (%s) too long (max is 8 char)" %
pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt = "run %s" % pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE, "PTC")
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode == "TRACKING" or hotlidmode == "CONSTANT"
assert (hotlidmode == "TRACKING" and hotlidtemp >= 0
and hotlidtemp <= 45) or (hotlidmode == "CONSTANT"
and hotlidtemp > 30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d' %
(pgm, hotlidmode, hotlidtemp, volume))
self.pgmStartTime = clock.pipetting
self.pgmEndTime = duration * 60 + clock.pipetting
self.ptcrunning = True
Sample.addallhistory("{%s}" % pgm,
addToEmpty=False,
onlyplate=decklayout.SAMPLEPLATE.name,
type="ptc")
if waitForCompletion:
self.waitpgm()
def waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime - clock.pipetting > 120:
# Run any idle programs
oldElapsed = clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime - clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime - clock.pipetting - 120)
if oldElapsed == clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime += (clock.pipetting - self.pgmStartTime)
clock.thermotime += (self.pgmEndTime - clock.pipetting)
clock.pipetting = self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
self.ptcrunning = False
self.moveplate(decklayout.SAMPLEPLATE, "Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.SAFETOEND, False,
worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.ENDTOSAFE, False,
worklist.OPEN, worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15, 1, 5, True)
def shake(self,
plate,
dur=60,
speed=None,
accel=5,
returnPlate=True,
samps=None):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps = Sample.getAllOnPlate(plate)
if samps is None:
samps = allsamps
if all([x.isMixed() for x in samps]):
print "No need to shake ", plate
maxvol = max([x.volume for x in allsamps])
minvol = min([x.volume for x in samps if not x.isMixed()] + [200])
(minspeed, maxspeed) = plate.getmixspeeds(
minvol * 0.95, maxvol + 5) # Assume volumes could be off
if minspeed > maxspeed:
print "minspeed(", minspeed, ") > maxspeed (", maxspeed, ")"
if speed is None:
if minspeed < maxspeed:
speed = (maxspeed + minspeed) / 2
else:
speed = maxspeed
warned = False
if speed > maxspeed:
print "WARNING: %s plate contains wells with up to %.2f ul, which may spill at %d RPM: " % (
plate.name, maxvol, speed),
for x in samps:
tmp = plate.getmixspeeds(x.volume, x.volume)
if tmp[1] < speed:
print "%s[%.1ful, max=%.0f RPM] " % (x.name, x.volume,
tmp[1]),
print
warned = True
if globals.verbose and speed < minspeed:
print "NOTICE: %s plate contains unmixed wells that may not be mixed at %d RPM: " % (
plate.name, speed),
for x in samps:
if x.isMixed():
continue
tmp = plate.getmixspeeds(x.volume * 0.95, x.volume + 5)
if speed < tmp[0]:
print "%s[%.1ful, min=%.0f RPM, max=%.0f RPM] " % (
x.name, x.volume, tmp[0], tmp[1]),
print
warned = True
if warned or globals.verbose:
print " Mixing %s at %.0f RPM (min unmixed vol=%.0ful -> min RPM=%.0f; max vol=%.0ful -> max RPM=%.f)" % (
plate.name, speed, minvol, minspeed, maxvol, maxspeed)
oldloc = plate.curloc
self.moveplate(plate, "Shaker", returnHome=False)
global __shakerActive
__shakerActive = True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d" % speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d" % accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name, speed)
Sample.addallhistory("(S%d@%.0f)" % (dur, speed), onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel + 4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive = False
if returnPlate:
self.moveplate(plate, oldloc)
def shake(self,plate,dur=60,speed=None,accel=5,returnPlate=True,samps=None,force=False):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps=Sample.getAllOnPlate(plate)
if samps is None:
samps=allsamps
if all([x.isMixed() for x in samps]) and not force:
logging.notice( "No need to shake "+plate.name+", but doing so anyway.")
minspeed=0
maxspeed=2000
for x in samps:
(a,b)=x.getmixspeeds()
minspeed=max([a,minspeed])
maxspeed=min([b,maxspeed])
if speed is None:
if minspeed<maxspeed:
speed=max((maxspeed+minspeed)/2,maxspeed-50) # Mix as fast as safely possible (but always above minspeed)
else:
speed=maxspeed
if speed<minspeed-2 or speed>maxspeed+2:
others=""
for x in allsamps:
(a,b)=x.getmixspeeds()
if b<minspeed or a>maxspeed:
if a is not None and a>0:
others+=" {%s: %.1ful,G=%.2f%%,min=%.0f,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,a,b)
else:
others+=" {%s: %.1ful,G=%.2f%%,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,b)
logging.mixwarning("Mixing %s at %.0f RPM; minspeed(%.0f) > maxspeed(%.0f), limits=[%s]"%(plate.name,speed,minspeed,maxspeed,others))
else:
logging.notice("Mixing %s at %.0f RPM ( min RPM=%.0f, max RPM=%.f)"%(plate.name, speed, minspeed, maxspeed))
oldloc=plate.curloc
self.moveplate(plate,"Shaker",returnHome=False)
global __shakerActive
__shakerActive=True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d"%speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d"%accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name,speed)
Sample.addallhistory("(S%d@%.0f)"%(dur,speed),onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel+4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive=False
if returnPlate:
self.moveplate(plate,oldloc)
def shake(self,plate,dur=60,speed=None,accel=5,returnPlate=True,samps=None):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps=Sample.getAllOnPlate(plate)
if samps is None:
samps=allsamps
if all([x.isMixed() for x in samps]):
print "No need to shake ",plate
maxvol=max([x.volume for x in allsamps])
minvol=min([x.volume for x in samps if not x.isMixed() ]+[200])
(minspeed,maxspeed)=plate.getmixspeeds(minvol*0.95,maxvol+5) # Assume volumes could be off
if minspeed>maxspeed:
print "minspeed(",minspeed,") > maxspeed (",maxspeed,")"
if speed is None:
if minspeed<maxspeed:
speed=(maxspeed+minspeed)/2
else:
speed=maxspeed
warned=False
if speed>maxspeed:
print "WARNING: %s plate contains wells with up to %.2f ul, which may spill at %d RPM: "%(plate.name, maxvol, speed),
for x in samps:
tmp=plate.getmixspeeds(x.volume,x.volume)
if tmp[1]<speed:
print "%s[%.1ful, max=%.0f RPM] "%(x.name,x.volume,tmp[1]),
print
warned=True
if globals.verbose and speed<minspeed:
print "NOTICE: %s plate contains unmixed wells that may not be mixed at %d RPM: "%(plate.name, speed),
for x in samps:
if x.isMixed():
continue
tmp=plate.getmixspeeds(x.volume*0.95,x.volume+5)
if speed<tmp[0]:
print "%s[%.1ful, min=%.0f RPM, max=%.0f RPM] "%(x.name,x.volume,tmp[0],tmp[1]),
print
warned=True
if warned or globals.verbose:
print " Mixing %s at %.0f RPM (min unmixed vol=%.0ful -> min RPM=%.0f; max vol=%.0ful -> max RPM=%.f)"%(plate.name, speed, minvol, minspeed, maxvol, maxspeed)
oldloc=plate.curloc
self.moveplate(plate,"Shaker",returnHome=False)
global __shakerActive
__shakerActive=True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d"%speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d"%accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name,speed)
Sample.addallhistory("(S%d@%.0f)"%(dur,speed),onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel+4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive=False
if returnPlate:
self.moveplate(plate,oldloc)
def shake(self,
plate,
dur=60,
speed=None,
accel=5,
returnPlate=True,
samps=None,
force=False):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps = Sample.getAllOnPlate(plate)
if samps is None:
samps = allsamps
if all([x.isMixed() for x in samps]) and not force:
logging.notice("No need to shake " + plate.name +
", but doing so anyway.")
minspeed = 0
maxspeed = 2000
for x in samps:
(a, b) = x.getmixspeeds()
minspeed = max([a, minspeed])
for x in allsamps:
(a, b) = x.getmixspeeds()
maxspeed = min([b, maxspeed])
if speed is None:
if minspeed < maxspeed:
speed = max(
(maxspeed + minspeed) / 2, maxspeed - 50
) # Mix as fast as safely possible (but always above minspeed)
else:
speed = maxspeed
if speed < minspeed - 2 or speed > maxspeed + 2:
others = ""
for x in allsamps:
(a, b) = x.getmixspeeds()
if b < minspeed or a > maxspeed:
if a is not None and a > 0:
others += " {%s: %.1ful,G=%.2f%%,min=%.0f,max=%.0f}" % (
x.name, x.volume, x.glycerolfrac() * 100, a, b)
else:
others += " {%s: %.1ful,G=%.2f%%,max=%.0f}" % (
x.name, x.volume, x.glycerolfrac() * 100, b)
logging.mixwarning(
"Mixing %s at %.0f RPM; minspeed(%.0f) > maxspeed(%.0f), limits=[%s]"
% (plate.name, speed, minspeed, maxspeed, others))
else:
logging.notice(
"Mixing %s at %.0f RPM ( min RPM=%.0f, max RPM=%.f)" %
(plate.name, speed, minspeed, maxspeed))
oldloc = plate.curloc
self.moveplate(plate, "Shaker", returnHome=False)
global __shakerActive
__shakerActive = True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d" % speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d" % accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name, speed)
Sample.addallhistory("(S%d@%.0f)" % (dur, speed),
onlyplate=plate.name,
type="shake")
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel + 4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive = False
if returnPlate:
self.moveplate(plate, oldloc)